Extrude Region (Vertex Normals) Extruding faces individually
Most likely you have the pivot center set to "individual origins." This causes each face to extrude along its own normal axis.



However, this wouldn't normally cause the problem you are having. The only reason it is causing it in this case is because you have duplicate geometry. This is most likely because of failed attempts at extrusion. DO NOT just right click and assume the extrude ended. It actually duplicated everything and "extruded", but didn't move anything, and kept it all where it was. So now there are two vertices where there was one. Just undo after you have one you don't like. That's the easiest safe way to get rid of an extrude. You can see this in my example scene, extruding to identical meshes, except one I "canceled" one extrude between each face. This means there is duplicate geometry on the upper object.



By simply dragging the face out you can see what I mean by extra geometry. You could see by the little dot in the middle of the edge that there was another face taking up "zero space", right on top of itself. When I pull away the main face it stretches the extra face out so you can see it. This unselected extra face is what's causing your problem.